+Open data
-Basic information
Entry | Database: PDB / ID: 2y4j | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH LACTATE | ||||||||||||
Components | MANNOSYLGLYCERATE SYNTHASE | ||||||||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / GT FAMILY 78 MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE | ||||||||||||
Function / homology | Function and homology information mannosylglycerate synthase / mannosylglycerate synthase activity / mannosylglycerate biosynthetic process / hexosyltransferase activity / identical protein binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | RHODOTHERMUS MARINUS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Nielsen, M.M. / Suits, M.D.L. / Yang, M. / Barry, C.S. / Martinez-Fleites, C. / Tailford, L.E. / Flint, J.E. / Davis, B.G. / Davies, G.J. / Gilbert, H.J. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase. Authors: Nielsen, M.M. / Suits, M.D.L. / Yang, M. / Barry, C.S. / Martinez-Fleites, C. / Tailford, L.E. / Flint, J.E. / Dumon, C. / Davis, B.G. / Gilbert, H.J. / Davies, G.J. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2y4j.cif.gz | 171.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2y4j.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 2y4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y4j_validation.pdf.gz | 462.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2y4j_full_validation.pdf.gz | 470.3 KB | Display | |
Data in XML | 2y4j_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 2y4j_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y4j ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4j | HTTPS FTP |
-Related structure data
Related structure data | 2y4kC 2y4lC 2y4mC 2bo7S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 5
NCS ensembles :
|
-Components
#1: Protein | Mass: 44714.789 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-382 Source method: isolated from a genetically manipulated source Details: TRUNCATION / Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): TUNER References: UniProt: Q9RFR0, mannosyl-3-phosphoglycerate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | LACTATE (LAC): LACTATE IS A MANNOSE ACCEPTOR | Sequence details | C-TERMINAL TRUNCATION | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5 Å3/Da / Density % sol: 75.3 % / Description: NONE |
---|---|
Crystal grow | pH: 5 Details: 0.3 M SODIUM D-LACTATE, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6, 40% (V/V) 2-METHYL-1, 3-PROPANEDIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→67 Å / Num. obs: 83970 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.4 / % possible all: 96.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BO7 Resolution: 2.3→129.02 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.317 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.807 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→129.02 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|